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BMRB: 16345

2KJW

Solution structure and backbone dynamics of the permutant P54-55

Authors

Ohman, A., Oliveberg, M., Oman, T.

Assembly

permutant P54-55

Entity

1. permutant P54-55 (polymer, Thiol state: not present), 96 monomers, 11244.77 Da Detail

MDPQGYFLWY QVEMPEDRVN DLARELRIRD NVRRVMVVAS TTPGRYEVNI VLNPNLDQSQ LALEKEIIQR ALENYGARVE KVEELGLRRL AYPIAK

Formula weight

11244.77 Da

Source organism

Thermus thermophilus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.7 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1041 of 1160)	88.5 % (541 of 611)	89.2 % (398 of 446)	99.0 % (102 of 103)
Backbone	98.1 % (555 of 566)	99.0 % (189 of 191)	97.2 % (276 of 284)	98.9 % (90 of 91)
Sidechain	84.1 % (577 of 686)	83.8 % (352 of 420)	83.9 % (213 of 254)	100.0 % (12 of 12)
Aromatic	29.0 % (18 of 62)	41.9 % (13 of 31)	13.3 % (4 of 30)	100.0 % (1 of 1)
Methyl	98.4 % (120 of 122)	98.4 % (60 of 61)	98.4 % (60 of 61)

1. permutant P54-55

MDPQGYFLWY QVEMPEDRVN DLARELRIRD NVRRVMVVAS TTPGRYEVNI VLNPNLDQSQ LALEKEIIQR ALENYGARVE KVEELGLRRL AYPIAK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.8 ~ 1.2 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	entity	natural abundance		0.8 ~ 1.2 mM
7	sodium chloride	natural abundance		50 mM
8	D2O	natural abundance		100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.24 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.93 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KJW, Strand ID: A Detail

Release date

2009-12-15

Citation

The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein-folding pathway
Haglund, E., Lind, J., Oman, T., Ohman, A., Maler, L., Oliveberg, M.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 21619-21624, PubMed 19966220 , DOI 10.1073/pnas.0907665106 , Abstract

Related entities 1. permutant P54-55, : 1 : 13 : 2 entities Detail

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

4 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

5 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

6 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

7 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

8 3D HN(CO)CA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

9 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

10 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N]		0.8 ~ 1.2 mM
10	MES	natural abundance		20 mM
11	sodium chloride	natural abundance		50 mM
12	H2O	natural abundance		95 %
13	D2O	natural abundance		5 %

11 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.8 ~ 1.2 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

12 3D 1H-15N TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.8 ~ 1.2 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

13 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.8 ~ 1.2 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

14 3D HNHA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.8 ~ 1.2 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

15 2D DQF-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	entity	natural abundance		0.8 ~ 1.2 mM
7	sodium chloride	natural abundance		50 mM
8	D2O	natural abundance		100 %

16 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	entity	natural abundance		0.8 ~ 1.2 mM
7	sodium chloride	natural abundance		50 mM
8	D2O	natural abundance		100 %

17 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	entity	natural abundance		0.8 ~ 1.2 mM
7	sodium chloride	natural abundance		50 mM
8	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16345_2kjw.nef
Input source #2: Coordindates	2kjw.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90------
MDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVASTTPGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVASTTPGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_16345_2kjw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1036		100.0 (chain: A, length: 96)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	898 (1)	noe	93.8 (chain: A, length: 96)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	153 (153)	.	100.0 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 539
  - ¹³C chemical shifts: 393
  - ¹⁵N chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 93.8%
- Total number of restraints: 897
- Weight of restraints: 1.0 (897)
- Potential type of restraints: square-well-parabolic (897)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
- Total number of restraints: 153
- Total number of restraints per polymer type: 153
- Weight of restraints: 1.0 (153)
- Potential type of restraints: square-well-parabolic (153)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords backbone dynamics, NMR, S6, solution structure, folding, S6 permutant